Computational and experimental insights into the structure and dynamics of heterochromatin

对异染色质结构和动力学的计算和实验见解

• 批准号: 10731977
• 负责人: Nathaniel A. Hathaway
• 金额: $ 24.56万
• 依托单位: UNIVERSITY OF MISSOURI-COLUMBIA
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-12-01 至 2024-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10731977
• 关键词: Algorithms; Architecture; Behavior; Binding; Biochemical Reaction; Biological Assay; Biology; Calibration; Cell Culture Techniques; Cells; Chemical Structure; Chemicals; Chromatin; Chromatin Fiber; Chromatin Structure; Complement; Complex; Computer Models; DNA; Data; Data Set; Development; Disease; Doxycycline; Enzymes; Epigenetic Process; Equilibrium; Event; Feedback; Fiber; Gene Expression Profiling; Genes; Goals; Grain; Heterochromatin; Individual; Investigation; Knowledge; Language; Lentivirus Vector; Life; Malignant Neoplasms; Measures; Mediating; Methodology; Methods; Modeling; Molecular; Molecular Profiling; Mus; Pathogenesis; Pathway interactions; Phase; Physics; Physiological; Process; Production; Proteins; Regenerative Medicine; Regulatory Element; Repression; Research; Resolution; Role; Running; Signal Transduction; Sirolimus; Stem cell pluripotency; Stochastic Processes; Structure; System; Technology; Testing; Time; Tretinoin; Visualization; Work; cancer therapy; chromosome conformation capture; computational platform; computerized tools; derepression; embryonic stem cell; experimental study; gene repression; heterochromatin-specific nonhistone chromosomal protein HP-1; improved; in vivo; induced pluripotent stem cell; insight; interest; mechanical properties; methylation pattern; migration; overexpression; particle; physical property; promoter; protein protein interaction; real time monitoring; recruit; response; simulation; small hairpin RNA; temporal measurement

Abstract Chemical, molecular and structural transformations of chromatin are intimately involved in critical cellular phenomena, including differentiation, signaling, and pathogenesis. A detailed knowledge of how molecular complexes involving multiple kilobases of DNA and hundreds of proteins respond to the finest changes in chemical structure is key to elucidating the role of chromatin transformations in life and disease. The overarching goal of this project is to develop and apply computational tools to investigate how the structure and dynamics of chromatin determine its functional states. Our central hypothesis is that physical properties and behavior of the chromatin fiber and associated proteins lend themselves to encoding into efficient and useful ultra-coarse- grained (UCG) representations. Our strategy to reach the goal is by bridging together several computational and experimental methodologies. We initiated the development of Molecular Biosystems (MB), a computational platform for UCG simulations specifically adapted to the chromatin biology. MB methodology represents a blend of physics-based mechanisms, such as dynamics of the chromatin fiber, with stochastic processes encompassing protein-protein interactions and enzymatic reactions. MB studies will be complemented by all-atom MD and CG simulations and experimentally tested using a unique chromatin in vivo assay (CiA) methodology. Specifically, we will investigate the chromatin-mediated repression of Oct4, a key gene regulating embryonic stem (ES) cell pluripotency at defined points in mammalian development. This is important because the ability to reverse the Oct4 repression would streamline production of induced pluripotent cells (iPSC) and advance regenerative medicine. The CiA technology at the Oct4 locus in mouse ES cells will be used for the exploration of changes to chromatin structure, as well as for testing the adequacy of MB simulations. Experimental endpoints that are directly comparable to computational hypotheses will be produced: (1) fraction of Oct4-repressed cells in cell culture; (2) H3K9 methylation patterns on Oct4 promoter; and (3) chromatin conformation capture. Three main components of our research are: (i) Extending and enhancing the UCG MB approach; (ii) Multi- scale simulations of chromatin processes to elucidate the structure and dynamics of heterochromatin of Oct4 regulatory elements; (iii) Experimental real-time monitoring of heterochromatin molecular signatures using Chromatin in vivo Assay (CiA) to study mechanisms and time course of Oct4 de-repression and provide feedback for the computational models. This work is important because of its focus on the physics of the gene repression, whose understanding will bring us one step forward toward the promise of regenerative medicine and new prospects for cancer therapy.

抽象的 染色质的化学，分子和结构转化密切参与关键细胞 现象，包括分化，信号传导和发病机理。关于分子如何的详细知识 涉及多个千射线酶DNA和数百种蛋白质的复合物应对最大的变化 化学结构是阐明染色质转化在生命和疾病中的作用的关键。总体 该项目的目标是开发和应用计算工具，以研究如何调查结构和动态 染色质确定其功能状态。我们的核心假设是物理特性和行为 染色质纤维和相关的蛋白质使其自身编码为高效且有用的超质量 粒度（UCG）表示。我们实现目标的策略是将几个计算和 实验方法。我们启动了分子生物系统（MB）的发展，这是一种计算 UCG模拟平台专门适用于染色质生物学。 MB方法论代表一种混合 基于物理的机制，例如染色质纤维的动力学，并具有随机过程 蛋白质蛋白质相互作用和酶促反应。 MB研究将由全原子MD和CG进行补充 使用独特的体内染色质分析（CIA）方法进行了模拟和实验测试。 具体而言，我们将研究OCT4的染色质介导的抑制，OCT4是调节胚胎的关键基因 在哺乳动物发育中定义的点处的茎（ES）细胞多能性。这很重要，因为能力 为了扭转OCT4的抑制作用将简化诱导的多能细胞（IPSC）的产生并推进 再生医学。小鼠ES细胞中OCT4基因座的CIA技术将用于探索 染色质结构的变化以及测试MB模拟的适当性。实验端点 将产生与计算假设的直接相当 在细胞培养中； （2）OCT4启动子上的H3K9甲基化模式； （3）染色质构象捕获。 我们研究的三个主要组成部分是：（i）扩展和增强UCG MB方法； （ii）多 染色质过程的比例模拟，以阐明OCT4异染色质的结构和动力学 监管元素； （iii）使用实验实时监测异染色质分子特征 体内染色质分析（CIA）研究OCT4消除抑制的机制和时间过程并提供反馈 对于计算模型。 这项工作很重要，因为它专注于基因抑制的物理，其理解将会 使我们朝着再生医学和癌症治疗的新前景迈出一步。

项目成果

Integrating DNA-encoded chemical libraries with virtual combinatorial library screening: Optimizing a PARP10 inhibitor.

• DOI: 10.1016/j.bmcl.2020.127464
• 发表时间: 2020-10-01
• 期刊: Bioorganic & medicinal chemistry letters
• 影响因子: 2.7
• 作者: Lemke M;Ravenscroft H;Rueb NJ;Kireev D;Ferraris D;Franzini RM
• 通讯作者: Franzini RM

A simulation model of heterochromatin formation at submolecular detail.

• DOI: 10.1016/j.isci.2022.104590
• 发表时间: 2022-07-15
• 期刊: ISCIENCE
• 影响因子: 5.8
• 作者: Williams, Michael R.;Xiaokang, Yan;Hathaway, Nathaniel A.;Kireev, Dmitri
• 通讯作者: Kireev, Dmitri